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Requeue a pipeline run ICAv2

The script relaunch_pipeline.py can also be run in a Docker container keng404/ica_pipeline_relaunch:0.0.1. This script was developed in an environment where python >= 3.9.

You can requeue pipeline runs

  • By specifying the user_reference/analysis_id and the corresponding project_name/project_id along with your API_KEY file or your API_KEY as a string

Below is a 'minimal' example command line:

python3 relaunch_pipeline.py --user_reference <USER_RUN_REFERENCE> --project_name <ICA_PROJECT_NAME> --api_key_file <PATH_TO_API_KEY_FILE>|--api_key <API_KEY>

or

python3 relaunch_pipeline.py --analysis_id <ANALYSIS_ID> --project_name <ICA_PROJECT_NAME> --api_key_file <PATH_TO_API_KEY_FILE>|--api_key <API_KEY>

You can also create API and CLI templates

ICA CLI template generation

python3 relaunch_pipeline.py --user_reference <USER_RUN_REFERENCE> --project_name <ICA_PROJECT_NAME> --api_key_file <PATH_TO_API_KEY_FILE>|--api_key <API_KEY> --create_cli_template

This command will print out a CLI template you can copy + paste to requeue a pipeline run. You can modify this template before running. As a convenience, a text file is saved with the CLI command for future reference.

ICA API template generation

python3 relaunch_pipeline.py --user_reference <USER_RUN_REFERENCE> --project_name <ICA_PROJECT_NAME> --api_key_file <PATH_TO_API_KEY_FILE>|--api_key <API_KEY> --create_api_template

This command will save a API JSON template you can copy + paste to requeue a pipeline run. You can modify this template before running. As a convenience, a text file is saved with the API command for future reference.

The JSON file will have two fields, header and data, that you can pass as a POST request to the ICA API endpoints for CWL or Nextflow analyses.

Additional guidance

  • Any pre-requisites/modules you need should be found here
  • If you have any spaces or special characters in your user_reference, project_name, or api_key, you may want to wrap those arguments in single quotes.
    • to be fair this scenario needs to be tested more rigorously. Underscores and dashes should be fine.

Limitations

This script will not work for any pipelines where users have used an inputJSON to provide inputData and parameters.

Additionally, the ICA CLI is not installed, so even though you can generate a CLI template, you should run it where you have your ICA CLI installed.